The first church, a wooden one, was built around 1643 for the Discalced Carmelite Order. This was burned down by the Swedes and Germans during the 1650 siege of Warsaw. A new building was founded in 1661 with most of the work occurring between 1692 and 1701. The façade was restricted after 1761 to its current appearance with columns and solid cornice.

Frederick Chopin got his first job at the Carmelite Church, giving a recital on the church's organ.

After the failed 1864 Uprising was crushed by the Russians the Tsarist Regime liquidated the monastery as it was "a stronghold of Polish patriotism". Unusually the Church survived World War II with only minimal damage and it served as the Cathedral whilst St. John's Cathedral was rebuilt from the ground up.